Description Details Objects from the Class Slots Methods Examples
Class object for storing all the information for a miRNA-mRNA correlation analysis.
In this version, miRNAs should be preferntially named according to miRBase 17, and mRNAs should be named according to HUGO gene symbol nomenclature.
Objects can be created by calls of the form new("corObject", ...)
.
dat.miRNA
:Object of class "matrix"
. Contains the miRNA expression (rows for miRNAs and columns for samples).
dat.mRNA
:Object of class "matrix"
. Contains the mRNA expression (rows for mRNAs and columns for samples).
pheno.miRNA
:Object of class "data.frame"
. Rows for samples and columns for phenotypical information.
pheno.mRNA
:Object of class "data.frame"
. Rows for samples and columns for phenotypical information.
cor
:Object of class "matrix"
. Rows for miRNAs and columns for mRNAs.
pval
:Object of class "matrix"
. Rows for miRNAs and columns for mRNAs.
net
:Object of class "data.frame"
. Rows for unique miRNA:mRNA pairs and columns for their corresponding information (at least: miRNA name, mRNA name, coefficient of correlation and p value).
diffexp.miRNA
:Object of class "data.frame"
. Rows for miRNAs and columns for their corresponding infomation (usually FC, logratio, mean expression, p value and corrected p value).
diffexp.mRNA
:Object of class "data.frame"
. Rows for mRNAs and columns for their corresponding infomation (usually FC, logratio, mean expression, p value and corrected p value).
sig.miRNA
:Object of class "vector"
. Vector specifying the miRNAs that are used for correlation.
sig.mRNA
:Object of class "vector"
. Vector specifying the mRNAs that are used for correlation.
GO.results
:Object of class "list"
. It contains the results of a GO analysis.
info
:Object of class "list"
. It contains the information of the tests and functions used.
No methods defined with class "corObject" in the signature.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | ## minimal corObject:
data(miRNA)
data(mRNA)
data(pheno.miRNA)
data(pheno.mRNA)
minimal<-new("corObject",dat.miRNA=miRNA,dat.mRNA=mRNA,
pheno.miRNA=pheno.miRNA,pheno.mRNA=pheno.mRNA)
str(minimal)
## corObject with more slots:
data(data.obj)
str(data.obj)
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